Research Projects

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Bacterial Interactions

Simon van Vliet, Alma Dal Co, Alejandra Rodriguez

The fast majority of bacteria live in dense communities such as biofilms. Cells in these communities often specialize to perform different tasks, either because of genetic differences in multi-species biofilms or because of phenotypic differences in clonal populations. The dynamics of these communities often depends critically on interactions between these specialized cells. We are interested in understanding how such interactions affect the dynamics of these communities. We approach this problem at different organizational levels: at the smallest scale - in clonal populations - we investigate if and how the phenotype of a cell depends on that of its neighbors. Furthermore, we study how the spatial-arrangements of cells performing different tasks affect the dynamics of the population. At a larger organizational level, we investigate how the community dynamics in multi-species biofilms depend on the frequency of environmental fluctuations. We address these questions using a combination of mathematical modeling, experimental evolution, microfluidics and quantitative single-cell experiments, using E. coli and other genetic model systems.

Bacteria in fluctuating environment

Bacterial Life in Fluctuating Environments

Frank Schreiber, Daan Kiviet, Jenna Gallie, Clément Vulin

Microbes are regularly exposed to unpredictable changes in their environment that force them to phenotypically adjust in order to survive. We investigate strategies by which microbes cope with such environmental fluctuations. One strategy is phenotypic switching, whereby individuals within clonal populations express different phenotypes. We investigate when and why phenotypic variation is beneficial in a range of systems: metabolism in E. coli, N2-fixation in Klebsiella oxytoca and capsule production in Pseudomonas fluorescens. We follow the expression of the phenotype the level of single cells, and investigate the consequences of these cellular decisions on growth and survival. Experimental techniques include time-lapse fluorescence microscopy, microfluidics, nanoSIMS (nano-scale secondary ion mass spectrometry), experimental evolution, genetic engineering, metabolomics and growth assays. 

Cellular Memory in Bacteria

Roland Mathis, Susan Schlegel

Do single bacterial cells keep a memory of past events, and do they use this memory to inform their cellular decision making to better predict future conditions? Environmental conditions are ever-changing and often form patterns in time; organisms can encounter periods where unfavorable conditions are common, and other periods where they are rare. A cellular memory could allow bacteria to read temporal patterns to better cope with recurring unfavorable conditions. We are investigating cellular memory in bacterial stress response (working with Caulobacter crescentus exposed to osmotic stress and antibiotics) and in nutrient uptake (working with E. coli). We are interested in how the responses of single cells gives rise to history-dependent behavior at the population level. In addition, we are also interested in the celluar basis of bacterial memory, and specifically in the influence of processes in cell membranes on memory formation. We are addressing these questions using a combination of quantitative single-cell measurements in microfluidics devices, mathematical modeling and biochemical analysis.

Bacterial Responses to Adverse Conditions

Daniel Angst, Sandra Probst, Lei Sun, Alejandra Manjarrez

Most bacteria are exposed to a range of external stressors. We are interested in how external stressors inactivate and kill bacteria, and in how bacteria can evade inactivation and survive. We focus on two stressors, antibiotics and light. We are interested in the costs and benefits of the expression of dedicated antibiotics resistance genes; in the temporal dynamics of spontaneous mutations that confer resistance; in how (exactly) antibiotics impact survival and reproduction of single bacterial cells; and in how cell-cell can mediate antibiotics tolerance and eventually the evolution of resistance. Using light as a stressor, we are investigating synergistic effects of light of different wavelengths on bacterial inactivation, and in how bacteria can evade such synergistic effects and acquire tolerance. We address these questions using E. coli as a model system, and combining molecular microbiology, experimental evolution and single-cell analysis. 

Bacterial Modifications of the Environment

Konstanze Schiessl, Colette Bigosch

Bacteria secrete a multitude of compounds that serve to release and transport resources, suppress competitors, and promote movement These secretion strategies are ultimately an attempt of bacteria to modify their environment, and turn it into a more favorable place. Considering the small size of bacteria compared to the environments they inhabit, this seems like a daunting task: One would expect that often large amounts of compounds have to be secreted in order to have any substantial effect on the environment. Additionally, a large fraction of secreted substances can get lost, due to diffusion, degradation, or uptake by other bacteria. We want to find out why, despite these aspects, secretion strategies are nevertheless efficient for bacteria. We study the secretion of siderophores, iron chelating molecules, as an example and use the siderophores of Pseudomonas aeruginosa as a model system to investigate key factors of secretion systems.

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Tue Mar 28 13:53:29 CEST 2017
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